Businessmap.io - Businessmap is the most flexible software platform for outcomes-driven enterprise agility.
Hygger - Hygger - is an Agile project management tool with built-in prioritization.
KanbanFlow - KanbanFlow is a Lean project management tool allowing real-time collaboration between team members. Supports the Pomodoro technique for time tracking.
Kanban Tool - Simple and effective online application for visual project management.
GitHub for Atom - Git and GitHub integration right inside Atom
Trello - Infinitely flexible. Incredibly easy to use. Great mobile apps. It's free. Trello keeps track of everything, from the big picture to the minute details.